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- EMDB-15955: Structure of the IFT-A complex; IFT-A1 module -

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Basic information

Entry
Database: EMDB / ID: EMD-15955
TitleStructure of the IFT-A complex; IFT-A1 module
Map dataIFT-A1 module; unsharpened map
Sample
  • Complex: IFT-A complex; IFT-A1 module
    • Protein or peptide: WD repeat-containing protein 19
    • Protein or peptide: Intraflagellar transport protein 140 homolog
    • Protein or peptide: Intraflagellar transport protein 122 homolog
Function / homology
Function and homology information


smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / : / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis ...smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / : / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization / neural tube patterning / intraciliary retrograde transport / protein localization to ciliary membrane / embryonic camera-type eye development / intraciliary transport / establishment of protein localization to organelle / gonad development / regulation of cilium assembly / spinal cord dorsal/ventral patterning / photoreceptor connecting cilium / ciliary tip / Intraflagellar transport / camera-type eye morphogenesis / embryonic brain development / protein localization to cilium / non-motile cilium assembly / non-motile cilium / embryonic heart tube development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / nervous system process / motile cilium / embryonic forelimb morphogenesis / determination of left/right symmetry / embryonic limb morphogenesis / limb development / embryonic digit morphogenesis / receptor clustering / axoneme / cilium assembly / photoreceptor outer segment / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / ciliary basal body / neural tube closure / cell morphogenesis / cilium / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / centrosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 19 / Intraflagellar transport protein 140 homolog / Intraflagellar transport protein 122 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsHesketh SJ / Mukhopadhyay AG / Nakamura D / Toropova K / Roberts AJ
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
Wellcome Trust217186/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007202/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: IFT-A structure reveals carriages for membrane protein transport into cilia.
Authors: Sophie J Hesketh / Aakash G Mukhopadhyay / Dai Nakamura / Katerina Toropova / Anthony J Roberts /
Abstract: Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) ...Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
History
DepositionOct 12, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15955.png

Downloads & links

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Map

FileDownload / File: emd_15955.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIFT-A1 module; unsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.16845933 - 0.47634465
Average (Standard dev.)0.00014597371 (±0.0070780874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15955_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IFT-A1 module, half map A

Fileemd_15955_half_map_1.map
AnnotationIFT-A1 module, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IFT-A1 module, half map B

Fileemd_15955_half_map_2.map
AnnotationIFT-A1 module, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IFT-A complex; IFT-A1 module

EntireName: IFT-A complex; IFT-A1 module
Components
  • Complex: IFT-A complex; IFT-A1 module
    • Protein or peptide: WD repeat-containing protein 19
    • Protein or peptide: Intraflagellar transport protein 140 homolog
    • Protein or peptide: Intraflagellar transport protein 122 homolog

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Supramolecule #1: IFT-A complex; IFT-A1 module

SupramoleculeName: IFT-A complex; IFT-A1 module / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: WD repeat-containing protein 19

MacromoleculeName: WD repeat-containing protein 19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 153.639297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKRIFSLLEK TWLGAPIQFA WQKTSGNYLA VTGADYIVKI FDRHGQKRSE INLPGNCVAM DWDKDGDVLA VIAEKSSCIY LWDANTNKT SQLDNGMRDQ MSFLLWSKVG SFLAVGTVKG NLLIYNHQTS RKIPVLGKHT KRITCGCWNA ENLLALGGED K MITVSNQE ...String:
MKRIFSLLEK TWLGAPIQFA WQKTSGNYLA VTGADYIVKI FDRHGQKRSE INLPGNCVAM DWDKDGDVLA VIAEKSSCIY LWDANTNKT SQLDNGMRDQ MSFLLWSKVG SFLAVGTVKG NLLIYNHQTS RKIPVLGKHT KRITCGCWNA ENLLALGGED K MITVSNQE GDTIRQTQVR SEPSNMQFFL MKMDDRTSAA ESMISVVLGK KTLFFLNLNE PDNPADLEFQ QDFGNIVCYN WY GDGRIMI GFSCGHFVVI STHTGELGQE IFQARNHKDN LTSIAVSQTL NKVATCGDNC IKIQDLVDLK DMYVILNLDE ENK GLGTLS WTDDGQLLAL STQRGSLHVF LTKLPILGDA CSTRIAYLTS LLEVTVANPV EGELPITVSV DVEPNFVAVG LYHL AVGMN NRAWFYVLGE NAVKKLKDME YLGTVASICL HSDYAAALFE GKVQLHLIES EILDAQEERE TRLFPAVDDK CRILC HALT SDFLIYGTDT GVVQYFYIED WQFVNDYRHP VSVKKIFPDP NGTRLVFIDE KSDGFVYCPV NDATYEIPDF SPTIKG VLW ENWPMDKGVF IAYDDDKVYT YVFHKDTIQG AKVILAGSTK VPFAHKPLLL YNGELTCQTQ SGKVNNIYLS THGFLSN LK DTGPDELRPM LAQNLMLKRF SDAWEMCRIL NDEAAWNELA RACLHHMEVE FAIRVYRRIG NVGIVMSLEQ IKGIEDYN L LAGHLAMFTN DYNLAQDLYL ASSCPIAALE MRRDLQHWDS ALQLAKHLAP DQIPFISKEY AIQLEFAGDY VNALAHYEK GITGDNKEHD EACLAGVAQM SIRMGDIRRG VNQALKHPSR VLKRDCGAIL ENMKQFSEAA QLYEKGLYYD KAASVYIRSK NWAKVGDLL PHVSSPKIHL QYAKAKEADG RYKEAVVAYE NAKQWQSVIR IYLDHLNNPE KAVNIVRETQ SLDGAKMVAR F FLQLGDYG SAIQFLVMSK CNNEAFTLAQ QHNKMEIYAD IIGSEDTTNE DYQSIALYFE GEKRYLQAGK FFLLCGQYSR AL KHFLKCP SSEDNVAIEM AIETVGQAKD ELLTNQLIDH LLGENDGMPK DAKYLFRLYM ALKQYREAAQ TAIIIAREEQ SAG NYRNAH DVLFSMYAEL KSQKIKIPSE MATNLMILHS YILVKIHVKN GDHMKGARML IRVANNISKF PSHIVPILTS TVIE CHRAG LKNSAFSFAA MLMRPEYRSK IDAKYKKKIE GMVRRPDISE IEEATTPCPF CKFLLPECEL LCPGCKNSIP YCIAT GRHM LKDDWTVCPH CDFPALYSEL KIMLNTESTC PMCSERLNAA QLKKISDCTQ YLRTEEELEN LYFQSDYKDD DDK

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Macromolecule #2: Intraflagellar transport protein 140 homolog

MacromoleculeName: Intraflagellar transport protein 140 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 167.328312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALYYDHQIE APDAAGSPSF ISWHPVHPFL AVAYISTTST GSVDIYLEQG ECVPDTHVER PFRVASLCWH PTRLVLAVGW ETGEVTVFN KQDKEQHTMP LTHTADITVL RWSPSGNCLL SGDRLGVLLL WRLDQRGRVQ GTPLLKHEYG KHLTHCIFRL P PPGEDLVQ ...String:
MALYYDHQIE APDAAGSPSF ISWHPVHPFL AVAYISTTST GSVDIYLEQG ECVPDTHVER PFRVASLCWH PTRLVLAVGW ETGEVTVFN KQDKEQHTMP LTHTADITVL RWSPSGNCLL SGDRLGVLLL WRLDQRGRVQ GTPLLKHEYG KHLTHCIFRL P PPGEDLVQ LAKAAVSGDE KALDMFNWKK SSSGSLLKMG SHEGLLFFVS LMDGTVHYVD EKGKTTQVVS ADSTIQMLFY ME KREALVV VTENLRLSLY TVPPEGKAEE VMKVKLSGKT GRRADIALIE GSLLVMAVGE AALRFWDIER GENYILSPDE KFG FEKGEN MNCVCYCKVK GLLAAGTDRG RVAMWRKVPD FLGSPGAEGK DRWALQTPTE LQGNITQIQW GSRKNLLAVN SVIS VAILS ERAMSSHFHQ QVAAMQVSPS LLNVCFLSTG VAHSLRTDMH ISGVFATKDA VAVWNGRQVA IFELSGAAIR SAGTF LCET PVLAMHEENV YTVESNRVQV RTWQGTVKQL LLFSETEGNP CFLDICGNFL VVGTDLAHFK SFDLSRREAK AHCSCR SLA ELVPGVGGIA SLRCSSSGST ISILPSKADN SPDSKICFYD VEMDTVTVFD FKTGQIDRRE TLSFNEQETN KSHLFVD EG LKNYVPVNHF WDQSEPRLFV CEAVQETPRS QPQSANGQPQ DGRAGPAADV LILSFFISEE HGFLLHESFP RPATSHSL L GMEVPYYYFT RKPEEADRED EVEPGCHHIP QMVSRRPLRD FVGLEDCDKA TRDAMLHFSF FVTIGDMDEA FKSIKLIKS EAVWENMARM CVKTQRLDVA KVCLGNMGHA RGARALREAE QEPELEARVA VLATQLGMLE DAEQLYRKCK RHDLLNKFYQ AAGRWQEAL QVAEHHDRVH LRSTYHRYAG HLEASADCSR ALSYYEKSDT HRFEVPRMLS EDLPSLELYV NKMKDKTLWR W WAQYLESQ GEMDAALHYY ELARDHFSLV RIHCFQGNVQ KAAQIANETG NLAASYHLAR QYESQEEVGQ AVHFYTRAQA FK NAIRLCK ENGLDDQLMN LALLSSPEDM IEAARYYEEK GVQMDRAVML YHKAGHFSKA LELAFATQQF VALQLIAEDL DET SDPALL ARCSDFFIEH SQYERAVELL LAARKYQEAL QLCLGQNMSI TEEMAEKMTV AKDSSDLPEE SRRELLEQIA DCCM RQGSY HLATKKYTQA GNKLKAMRAL LKSGDTEKIT FFASVSRQKE IYIMAANYLQ SLDWRKEPEI MKNIIGFYTK GRALD LLAG FYDACAQVEI DEYQNYDKAH GALTEAYKCL AKAKAKSPLD QETRLAQLQS RMALVKRFIQ ARRTYTEDPK ESIKQC ELL LEEPDLDSTI RIGDVYGFLV EHYVRKEEYQ TAYRFLEEMR RRLPLANMSY YVSPQAVDAV HRGLGLPLPR TVPEQVR HN SMEDARELDE EVVEEADDDP ENLYFQSWSH PQFEK

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Macromolecule #3: Intraflagellar transport protein 122 homolog

MacromoleculeName: Intraflagellar transport protein 122 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.007734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA YAKDGKRFAS GSADKSVIIW TSKLEGILK YTHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH KSSSKIICCS WTNDGQYLAL GMFNGIISIR N KNGEEKVK ...String:
MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA YAKDGKRFAS GSADKSVIIW TSKLEGILK YTHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH KSSSKIICCS WTNDGQYLAL GMFNGIISIR N KNGEEKVK IERPGGSLSP IWSICWNPSS RWESFWMNRE NEDAEDVIVN RYIQEIPSTL KSAVYSSQGS EAEEEEPEEE DD SPRDDNL EERNDILAVA DWGQKVSFYQ LSGKQIGKDR ALNFDPCCIS YFTKGEYILL GGSDKQVSLF TKDGVRLGTV GEQ NSWVWT CQAKPDSNYV VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRIK CKELVKKIAI YRNR LAIQL PEKILIYELY SEDLSDMHYR VKEKIIKKFE CNLLVVCANH IILCQEKRLQ CLSFSGVKER EWQMESLIRY IKVIG GPPG REGLLVGLKN GQILKIFVDN LFAIVLLKQA TAVRCLDMSA SRKKLAVVDE NDTCLVYDID TKELLFQEPN ANSVAW NTQ CEDMLCFSGG GYLNIKASTF PVHRQKLQGF VVGYNGSKIF CLHVFSISAV EVPQSAPMYQ YLDRKLFKEA YQIACLG VT DTDWRELAME ALEGLDFETA KKAFIRVQDL RYLELISSIE ERKKRGETNN DLFLADVFSY QGKFHEAAKL YKRSGHEN L ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY ISAGEHVKAI EICGDHGWVD MLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAG RQREAVQVLE QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH R HTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP ARFQKSIELG TL TIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY LEEGITDEEA ISLIDLEVLR PKR DDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF EQGGSEFVPV VVSRLVLRSM SRRDVLIKRW PPPLRWQYFR SLLP DASIT MCPSCFQMFH SEDYELLVLQ HGCCPYCRRC KDDPGP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Details: Average electron dose for additional dataset was 49.5 (e-/A2)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model generated from the data
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Resolution range 7-15A / Number images used: 136617
FSC plot (resolution estimation)

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